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Matrix synthesis as a specific property of the living.

Matrix synthesis as a specific property of the living.

23.09.2019

To the question Matrix Synthesis it is given by the author Alena Avgustenyak the best answer is MATRIX SYNTHESIS IS
1. Polymerization and polycondensation, in which the structure of the resulting polymer and (or) the kinetics of the process are determined by other macromolecules (matrices) that are in the immediate vicinity. contact with molecules of one or several. monomers and growing chains. M.'s example with. in wildlife - the synthesis of nucleic acids and proteins, in which the role of the matrix is played by DNA and RNA, and the composition and order of alternation of links in the growing (daughter) chain are uniquely determined by the composition and structure of the matrix. The term "MS" is usually used when describing the synthesis of nucleic acids and proteins, and when considering methods for obtaining other polymers, terms such as matrix polyreactions, polymerization, and polycondensation are used.

Such M. s. is realized under the condition of chem. and steric. correspondence (complementarity) of the monomers and the growing chain, on the one hand, and the matrix, on the other; in this case, elementary acts are carried out between monomers and growing macromolecules (as well as oligomers - during matrix polycondensation) associated with the matrix. Typically, monomers and oligomers are reversibly bound to the matrix by fairly weak intermoles. interaction - electrostatic. , donor-acceptor, etc. Daughter chains are almost irreversibly associated with the matrix ("recognize" the matrix) only after they have reached a certain length, depending on the energy of the interaction. between the links of the matrix and the child chain. "Recognition" of the matrix by a growing chain is a necessary stage of M. s. ; daughter chains almost always contain a fragment or fragments formed according to the "ordinary" mechanism, i.e., without the influence of the matrix. M.'s speed with. can be higher, lower or equal to the rate of the process in the absence of a matrix (kinetic matrix effect). The structural matrix effect is manifested in the ability of the matrix to influence the length and chem. the structure of daughter chains (including their steric structure), and if in M. s. two or more monomers are involved - this also affects the composition of the copolymer and the way the units alternate. M.'s method with. polymer-polymer complexes are obtained that have a more ordered structure than polycomplexes synthesized by simple mixing of solutions of polymers, as well as polycomplexes, which cannot be obtained from ready-made polymers due to the insolubility of one of them. M. s. - a promising method for obtaining new polymeric materials. The term "MS" is usually used when describing the synthesis of nucleic acids and proteins, and when considering methods for obtaining other polymers, terms such as matrix polyreactions, polymerization, and polycondensation are used. Lit. : Kabanov V. A., Papisov I. M., "High-molecular compounds", ser. A, 1979, vol. 21, no. 2, p. 243-81; Painting by O. V. [and others], "DAN USSR", 1984, v. 275, No. 3, p. 657-60; Litmanovich A. A., Markov S. V., Papisov I. M., "High-molecular compounds", ser. A, 1986, v. 28, No. 6, p. 1271-78; Ferguson J., Al-Alawi S., Graumayen R., "European Polymer Journall", 1983, v. 19, no. 6, p. 475-80; Polowinski S., "J. Polymer. Sci.", Polimer Chemistry Edition, 1984, v. 22, no. 11, p. 2887-94. I. M. Papisov.
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As already mentioned (p. 59), the most important biopolymers - proteins and nucleic acids - are synthesized in a living organism by matrix polycondensation. For the implementation of the matrix synthesis of the polymer, it is necessary matrix macromolecule, bearing all information on the primary structure of the synthesized macromolecule. In the course of synthesis, this information is "read" and different monomers enter into synthesis reactions in a certain order. For this, it is necessary that each monomer "recognizes" the place on the macromolecule-matrix where the information about this particular monomer is "recorded". In other words, some structural conformity between the monomer molecule and the corresponding site of the matrix; this correspondence is called complementarity(in some Russian-language sources there is the spelling "set and mentality"; the point is probably that the English word Withomple mental pronounced like ' compli ment ry).

The principle of complementarity of the macromolecule-matrix and the synthesized polymer can be used to synthesize polymers with a certain primary structure any method (and polymerization  and polycondensation) research is underway on the matrix preparation of synthetic copolymers. However, to date, the only effective examples of matrix syntheses of polymers are the synthesis of proteins and nucleic acids by matrix polycondensation. All these syntheses take place during genetic processes, primarily - replication, transcription and broadcasts(the synthesis of small sections of DNA also occurs during another genetic process - repair).

In all these cases, the matrix is nucleic acid macromolecule: during replication and transcription - DNA, during translation - matrix (information) RNA. Complementary recognition is carried out: A. During replication and transcription (as well as repair) - between the nucleotide units of the matrix macromolecule and monomers (nucleoside triphosphates); B. During translation - between the nucleotide units of the macromolecule - matrix and the nucleotide units of anticodons. This recognition is carried out by the formation of hydrogen bonds between heterocyclic bases: for DNA in pairs of adenine-thymine (A-T, Ade-Thy) and guanine-cytosine (G-C, Gua-Cyt), for RNA - in pairs of adenine-uracil (A-U, Ade-Ura) and guanine-cytosine. In pairs A-T and A-U, two hydrogen bonds are formed, in a pair G-C - three:

These pairs are exactly the same size (1.085 nm); this makes it possible to construct regular secondary structures (primarily the DNA double helix).

Replication, transcription and translation start and end in strictly defined places matrix macromolecules (in other words, there are “start signal” and “stop signal” for matrix syntheses). The start of these processes is called initiation, the process of polymer chain formation is elongation the ending - termination. All these processes are catalyzed by several enzymes.

Replication. During this genetic process, doubling DNA molecules, i.e. copying genetic information. The essence of the process is the unwinding of the DNA double helix into single chains; each of them serves as a template for the synthesis of a new (daughter) chain from monomers - deoxyribonucleoside-5'-triphosphates. Synthesis catalyzed enzymes DNA polymerases who carry out linear synthesis (i.e., at each stage of chain formation, the polymer and monomer interact) in the 5’→3’ direction (i.e., at each stage, the 3’-terminal OH group of the polymer and the 5’-triphosphate group of the monomer react:

Since each monomer recognizes its own site, the daughter chain is an exact copy of the separated one [if during the synthesis, the “wrong” monomer (i.e., not complementary to its matrix unit) is added to the chain, then the enzyme carries out a correction - it splits off this link].

The double bond begins to unravel in some particular place; synthesis of daughter chains begins immediately after the beginning of the unwinding of the double helix; the double helix continues to unwind, and following the unwinding (movement of the “replicative fork”), the growth of child chains occurs. In this case, on two single chain-matrices synthesis proceeds according to different schemes. The fact is that in the double helix of the original (maternal) DNA, the chains are oriented antiparallel; so for one strand, the replication fork moves in the 5'→3' direction (this strand is called leading), and for the other - in the direction 3'→5' (this chain is called lagging behind). Since the synthesis of the daughter chain can go only in the direction 5'→3', then on leading chain it is synthesized in the same direction, which is the movement of the fork, and on lagging - in the opposite direction. Therefore, on the leading chain goes continuous synthesis "after" the movement of the fork, and on the lagging behind - intermittent, in the form of separate fragments, called fragments of Okazaki(while one fragment is being synthesized, the fork moves in the opposite direction and a place on the matrix is vacated; then the synthesis of this fragment stops, and the synthesis of the second fragment begins in the vacated place, etc.):

After the end of the synthesis, the Okazaki fragments are linked by special enzymes (ligases) into one chain. Thus, on one chain (leading) there is a purely linear synthesis, and on the other - lagging - block (convergent).

Daughter chains form with parent chains double helixes are copies of the original double helixes.

Polymerase chain reaction (amplification of DNA fragments)

Relatively recently (K. Mullis, 1988) a technique has been developed that allows a process similar to replication to be carried out not in the body, but “in a flask” ( in vitro) . Such a process is called polymerase chain reaction, PCR (Polymerase Chain reaction, PCR) . The polymerase chain reaction makes it possible to repeatedly increase the amount of initially taken DNA; such an increase in the number (reproduction) is usually denoted by the term " amplification". Not all native DNA is subjected to amplification by the PCR method, but its fragments containing genes of interest to the researcher. To obtain such fragments, native DNA is subjected to specific cleavage ( restrictions) special enzymes - restrictases(to be discussed later). Necessary condition for amplification: for the fragment to be amplified, the primary structure from the 3' ends of both chains to about 20-30 units should be known.

To carry out the polymerase chain reaction, it is necessary to have primers - oligonucleotides 20-30 units long, complementary primary structures of both chains from the 3' ends. The synthesis of such oligonucleotides is well developed.

For PCR, the amplifiable DNA fragment is placed in the reaction vessel, great excess both primers and monomers - deoxyribonucleotide - 5'-triphosphates - and DNA polymerase is introduced; usually use heat-resistant polymerase isolated from thermobacteria. The mixture is heated to 95 0 C; in this case, the double helix of the amplified DNA fragment breaks up into single chains; then quickly cooled to 60 0 С; while the primers coordinate with their complementary 3' ends of each strand. This is more likely than a re-creation of a broken double helix. primers are in large excess. Strand-associated primers serve as primers for DNA template synthesis from monomers, which is catalyzed by DNA polymerase. Synthesis goes in the direction 5'→3'; on each strand, a complementary second strand is synthesized and, consequently, the amount of DNA is doubled. Then the heating-cooling cycle is repeated; each of the DNA macromolecules doubles again, and so on. Thus, it is possible to carry out several cycles and multiply the amount of DNA; a large excess of primers and monomers allows this to be done. The PCR procedure is shown in the diagram below; for simplicity, primers are shown with a length of 7 links, although in reality they are noticeably longer (20-30 links):

The synthesis of polynucleotide chains proceeds, of course, according to the same scheme (polymer + monomer) as in conventional replication (p. 91).

Transcription. During this process, there is broadcast information from DNA to matrix(information) DNA (as well as transport and ribosomal RNA). The process has much in common with replication: a DNA macromolecule is a template for the synthesis of an RNA macromolecule from monomers - ribonucleoside-5’-triphosphates; synthesis also begins with the unwinding of the DNA double helix and proceeds in the direction 5' → 3' in a linear pattern when catalyzed by enzymes - RNA polymerases. However, there are also fundamental features: 1) Unlike replication, the matrix is only one chain original DNA (the so-called minus-strand); 2) The synthesized chain does not form a double helix with the matrix molecule, but separates in the form single chain; molecule - the template again forms a double helix with the previously detached DNA strand (plus strand): the DNA-DNA double helix is more stable than the DNA-RNA helix:

Both replication and transcription synthesize very high molecular weight polynucleotide chains with the highest speed(for eukaryotes - 1000-3000 links per minute, for prokaryotes - up to 50,000 thousand links per minute). BUT. Speed process is due to: 1. Accurate spatial orientation of reacting particles: the 5'-triphosphate group of the monomer is accurately brought to the 3'-OH-terminal link of the synthesized chain; this occurs in the process of complementary recognition; 2. Enzymatic catalysis which is known to be the most efficient. Matrix synthesis of nucleic acids, in contrast to non-matrix synthesis, does not require the protection of "extra groups": these factors ensure the absolute specificity of the interaction of functional groups. B. high molecular weight of the synthesized polymer is achieved complete removal low molecular weight reaction product - pyrophosphate, which is hydrolyzed to phosphate [as already mentioned (p. 72), the synthesis of nucleic acids refers to equilibrium polycondensation].

Broadcast. Matrix biosynthesis of polypeptides. During translation, genetic information is transferred from messenger RNA (mRNA) to protein.

The template for the synthesis of the polypeptide chain is the mRNA molecule; this raises the problem of translating information from the 4-letter "alphabet" of RNA to the 20-letter "alphabet" of the polypeptide chain (one of the meanings of the term "translation" is translation). In other words, the existence of a structural correspondence between certain sections of the RNA template and certain monomers is necessary for the synthesis of polypeptides - α-amino acids. This correspondence is called protein code. The code is triplet: each amino acid corresponds to a region of mRNA containing three nucleotide units; in other words, it is encoded triplet nucleotide links; such a triplet is called codon. The totality of all codons protein code.

The protein code is degenerate- most α-amino acids are encoded more than one codon. Codons that code for the same amino acid are called synonymous; as a rule, the first two links of synonymous codons are the same, and the third is different: for example, proline ( Pro) encoded by four codons: CCU, CCA, CCC, CCG. Of the 64 codons (this is the number of possible combinations of four types of units, three each), 61 encode α-amino acids, and three do not encode anything; they're called terminal or stop codons; on these sites of the matrix, the synthesis of the polypeptide stops. The code, as a rule, does not overlap, codons go “butt” one after another: if, for example, in the GAAUGUCCG sequence, the first three links (GAA) encode one amino acid, then the second three (UGU) encode the second, and the third (CCG) encode the third ; at the same time, for example, the AAU triplet is not a codon here.

The protein code was deciphered in the 1960s largely due to the use of synthetic matrices, products of oligonucleotide polycondensation (p. 89).

α-amino acids cannot directly recognize their corresponding codons, since there is no direct complementarity between their structures. Recognition is carried out with the help of molecules intermediaries(adapters, or quite in Russian - adapters) - molecules that can specifically coordinate on the one hand with codons, and on the other hand with their corresponding α-amino acids. These adapters are transfer RNAs(tRNA) - relatively low molecular weight polynucleotides (73-85 nucleotide units); these RNAs are soluble and highly mobile, which allows them to perform a transport function - the delivery of amino acids to the matrix. Transfer RNA has a specific spatial structure ("cloverleaf"); one of the fragments of this structure ("acceptor stem") specifically contacts hisα-amino acid (and only with it!); the other fragment (“anticodon loop”) contains a triplet of nucleotide units, complementary the codon that codes for that particular amino acid; this triple is called anticodon(for example, if an amino acid is encoded by the UCA triplet, then the anticodon in its tRNA is AGU).

Before the actual translation process, α-amino acids recognize “their” tRNAs and then covalently bind to them with the formation of an ester at the 3’-terminal link of the “acceptor stem” - aminoacyl-tRNA:

Covalent binding occurs with the participation of 5'-adenosine triphosphate (ATP, pppA), which supplies the energy necessary for this (cleaving to adenosine monophosphate and pyrophosphate). The formation of aminoacyl-tRNA is catalyzed by enzymes - aminoacyl-tRNA synthetases; each of them recognizes, on the one hand, “its own” α-amino acid, and, on the other hand, “its own” tRNA (“double control”, which practically excludes errors in recognition).

Further, t-RNA transports the α-amino acid associated with it to the matrix, where the “assembly” of the polypeptide chain takes place. The template, mRNA, forms a complex with ribosome- a cell organelle, which is a specific complex of ribosomal RNA with proteins. During synthesis, the ribosome moves along the mRNA chain from codon to codon (this movement is called translocation). It is on the ribosome that the synthesis of the polypeptide chain occurs. Omitting the description of the structure of the ribosome, we note that it has two binding centers – A-center(amino acid) and R-center(peptide), which are directly involved in the synthesis.

Again, omitting the beginning (initiation) of the translation process, let us consider a single cycle of elongation - a set of processes in which the polypeptide chain increases for one link(Fig. 9)

One elongation cycle includes three stages. Before the first stage, the P-center is occupied by tRNA associated with the C-terminal link of the emerging polypeptide chain; The A-center is free and located at the codon encoding next amino acid. On the first In step (1), the tRNA bound to this next amino acid (here, phenylalanine) recognizes the codon of that amino acid (using the anticodon) and coordinates with it, anchoring itself at the A-center. It is very important that the peptide chain at the P-center and the next amino acid precisely oriented in relation to each other - the NH 2 group of the next amino acid is precisely “targeted” at the ester carbonyl of the C-terminal unit of the peptide chain. This orientation is due to the specific structure of the ribosome. Accurate orientation allows very effective implementation of the key second stage (2) - peptide bond formation(condensation). This reaction proceeds according to the type of ester aminolysis; The "alcohol" component - tRNA - is displaced and remains at the P-center, and the peptide chain, which has lengthened by one link, is now associated with a new tRNA molecule attached to the A-center.

The formation of a peptide bond is catalyzed by an enzyme - peptidyl transferase - and proceeds at a very high speed - in the order of 10 -2 - 10 -3 sec.

Followed by third step (3), which consists of three steps. At the first stage, the released tRNA of the previous amino acid leaves the P-center (removal of a by-product of equilibrium polycondensation). At the second stage, tRNA with a peptide chain attached to it moves from the A-center to the freed P-center. Finally, at the third stage, the ribosome moves along the mRNA chain by one codon (to the right in the figure), i.e. going on translocation. After that, the picture is completely similar to the original one (before the start of the first stage), but the polypeptide chain has one more link, and a new codon is located next to the A-center; then everything repeats. One cycle of elongation takes about 0.05 seconds, so that the synthesis of a sufficiently large protein from 400 units takes 20 seconds. Synthesis proceeds in the direction of 5"->3" mRNA and from the N-terminus of the polypeptide chain to its C-terminus.

Termination translation occurs when the A-center of the ribosome hits the stop codon; synthesis stops, the finished polypeptide chain is separated from the last tRNA and leaves the ribosome.

Rice. 9. Scheme of one cycle of elongation during translation

Summary

Polycondensation processes in the vast majority of cases (with the exception of polyrecombination) are reduced to the interaction between the functional groups of monomers. If each monomer contains two groups, a linear polymer is formed (linear polycondensation), if three or more, crosslinking is possible to form a three-dimensional structure (three-dimensional polycondensation). End groups of polymers are unused functional groups of monomers.

For polycondensation, a wide variety of interactions between functional groups are used, of which, probably, the most common is polyacylation; according to this scheme, in particular, the synthesis of proteins occurs and, according to a similar scheme, the synthesis of nucleic acids.

Polycondensation reactions proceed according to stepwise mechanisms. Final resultlinear polycondensation is determined mainly by two factors: the degree of reversibility of the reaction and the ratio of the reacting groups. According to the degree of reversibility, equilibrium and nonequilibrium polycondensation are distinguished. In the first case, the reverse reactions (destructions) proceed to a noticeable extent, so it is necessary to remove the low molecular weight reaction product; in the second case, such removal is not necessary. The violation of the equivalence of the reacting groups in all cases limits the length of the polymer chain. Therefore, to achieve high molecular weights, it is necessary to ensure strict equivalence of groups; on the contrary, the calculated excess of one of the groups should be used to obtain oligomers. Forthree-dimensional polycondensation, these restrictions are not so significant, because for stitching, in many cases, an incomplete depth of the process is sufficient.

Conventional non-programmed polycondensation produces polymers with a high degree of polydispersity; however, the proportion of molecules of any size (both in number and in mass) can in many cases be calculated quite accurately.

On the other hand, it is polycondensation that makes it possible to carry out programmed syntheses, which result in the formation of monodisperse polymers, including copolymers with a given primary structure. These can be syntheses with control of each stage of polymer chain formation (synthesis of dendrimers, synthesis of polypeptides and polynucleotides “in test tube”). The most perfect variant of programmed synthesis is matrix synthesis, during which the information “recorded” on the matrix molecule is read. These are the processes of replication, transcription and translation; enzymatic catalysis and precise orientation of the reacting molecules make it possible to carry out these syntheses not only with the highest precision, but also with the highest speed.

A way of recording genetic information in a DNA molecule. Biological code and its properties.

genetic code - a method of recording information about protein amino acids using DNA nucleotides.

Properties:

1-tripletity (one a / c is encoded by three nucleotides, 3 nucleotides-triplet)

2-redundancy (some a / c are encoded in several triplets)

3-uniqueness (one a/k corresponds to each triplet)

4-universality (for all organizations on Earth, the genetic code is the same)

5-linearity (read sequentially)

6. Unique properties of DNA: self-doubling, self-healing of structures.

See questions 3 and 4

Matrix synthesis 3 types:

DNA synthesis - replication- self-replacement of mol-l DNA, which usually occurred before making cells. During replication, the mother mol-la untwisted, and the complement of its thread was disconnected (the image of the replication fork). Helicase breaks the hydrogen bond between complementary nucleotides and disconnects the strands, topoisomerase relieves the tension that arises in this case in the mol. The single strands of the mater mole serve as templates for the synthesis of daughter complement strands. With single strands, they bind SSB proteins (destabilizing proteins), which prevent them from connecting into a double helix. As a result of replication, the image is two identical molecules of DNA, completely repeating the mother of the mol. At the same time, each new mol-la consists of one new and one old chain. Complement strands of DNA molecules are antiparallel. The extension of the polynucleotide chain always occurred in the direction from the 5" end to the 3" end. As a result, one strand is leading (3" end at the base of the replication fork), and the other is lagging (5" end at the base of the fork), and therefore is built from Okazaki fragments growing from 5" to 3" end. Okazaki fragments are sections of DNA that are 100-200 nucleotides long in eukaryotes and 1000-2000 nucleotides in prokaryotes.

DNA chain synthesis is carried out by the enzyme DNA polymerase. It builds up a daughter chain, attaching to its 3 "end nucleotides that are complementary to the nucleotides of the parent chain. The peculiarity of DNA polymerase is that it cannot start working from scratch without having a 3" end of the daughter strand. Therefore, the synthesis of the leading strand and the synthesis of each Okazaki fragment is initiated by the primase enzyme. It is a type of RNA polymerase. Primase is able to start the synthesis of a new polynucleotide chain from the connection of two nucleotides. Primase synthesizes short primers from RNA nucleotides. Their length is about 10 nucleotides. To the 3" end of the primer, DNA polymerase begins to add DNA nucleotides.

The exonuclease enzyme removed the primers. DNA polymerase completes the Okazaki fragments, the enzyme ligase crosslinks them.

RNA synthesis - transcription- RNA synthesis on the DNA matrix (in eukaryotes in the nucleus, in prokaryotes in the cytoplasm). During transcription, a complementary copy of one of the DNA strands is built. As a result of transcription, mRNA, rRNA and tRNA are synthesized. Transcr-ju impl RNA polymerase. In eukaryotes, transcription is carried out by three different RNA polymerases:

RNA polymerase I rRNA synthesiser

RNA polymerase II mRNA synthesizer

RNA polymerase III tRNA synthesiser

RNA polymerase binds to a DNA molecule in the promoter region. A promoter is a segment of DNA that marks the start of transcription. It is located before the structural gene. By attaching to the promoter, RNA polymerase unwinds a section of the DNA double helix and section of the complementary chain. One of the two strands, the sense strand, serves as a template for RNA synthesis. RNA nucleotides are complementary to the nucleotides of the DNA sense strand. Transcription proceeds from the 5" end to its 3" end. RNA polymerase separates the synthesized RNA from the matrix and restores the DNA double helix. Transcription continues until the RNA polymerase reaches the terminator. A terminator is a DNA region that marks the end of transcription. Upon reaching the terminator, RNA polymerase separates from both the template DNA and the newly synthesized RNA molecule.

Transkr-I affairs on 3 stages:

Initiation-attach RNA polymerase and transcription factor proteins that help it to DNA and start their work.

Elongation- extension - polynucleotide th RNA chain.

Termination- the end of the synthesis of mol-ly RNA.

Protein synthesis - translation- the process of synthesis of the polypeptide chain passing on the ribosome. Occurs in the cytoplasm. The ribosome consists of two subunits: large and small. Subunits are built from rRNA and proteins. The non-acting ribosome is found in the cytoplasm in a dissociated form. The active ribosome is assembled from two subunits, while it contains active centers, including aminoacyl and peptidyl. In the aminoacyl center, the pattern of the peptide bond occurs. Transfer RNAs are specific, i.e. one tRNA can carry only one specific a/k. This a/k is encoded by a codon that is complementary to the tRNA anticodon. In the process of translation, the ribosome translates the sequence of mRNA nucleotides into the a / k sequence of the polypeptide chain.

Translation of cases into 3 stages.

Initiation- assembly of the ribosome on the initiating codon of mRNA and the beginning of its work. Initiation begins with the fact that a small subunit of the ribosome and tRNA, carrying methionine, is connected to mRNA, which corresponds to the initiating codon AUG. Then a large subunit is attached to this complex. As a result, the initiating codon ends up in the peptidyl center of the ribosome, and the first significant codon is located in the aminoacyl center. Various tRNAs approach it, and only the anticodon that is complementary to the codon will remain in the ribosome. Hydrogen bonds form between the complementary nucleotides of the codon and anticodon. As a result, two tRNAs are temporarily associated with mRNA in the ribosome. Each tRNA brought into the ribosome a / c, encrypted by an mRNA codon. There is a peptide bond between these a/k images. After that, the tRNA that brought the methionine separates from its a / c and from the mRNA and leaves the ribosome. The ribosome moves one triplet from the 5" end to the 3" end of the mRNA.

Elongation- the process of building up a polyp chain. Various tRNAs will fit into the aminoacyl center of the ribosome. The process of tRNA recognition and the process of forming a peptide bond will be repeated until a stop codon appears in the aminoacyl center of the ribosome.

Termination– completion of polypeptide synthesis and dissociation of the ribosome into two subunits. There are three stop codons: UAA, UAG and UGA. When one of them is in the aminoacyl center of the ribosome, a protein binds to it - a translation termination factor. This causes the collapse of the entire complex.

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1. Matrix synthesis reactions

In living systems, reactions are encountered that are unknown in inanimate nature - reactions of matrix synthesis.

The term "matrix" in technology refers to the form used for casting coins, medals, typographic type: the hardened metal exactly reproduces all the details of the form used for casting. Matrix synthesis is like casting on a matrix: new molecules are synthesized in exact accordance with the plan laid down in the structure of already existing molecules.

The matrix principle underlies the most important synthetic reactions of the cell, such as the synthesis of nucleic acids and proteins. In these reactions, an exact, strictly specific sequence of monomeric units in the synthesized polymers is provided.

Here there is a directed contraction of monomers to a certain place in the cell - to the molecules that serve as a matrix, where the reaction proceeds. If such reactions occurred as a result of a random collision of molecules, they would proceed infinitely slowly. The synthesis of complex molecules based on the matrix principle is carried out quickly and accurately.

The role of the matrix in matrix reactions is played by macromolecules of nucleic acids DNA or RNA.

Monomeric molecules from which the polymer is synthesized - nucleotides or amino acids - in accordance with the principle of complementarity are arranged and fixed on the matrix in a strictly defined, predetermined order.

Then there is a "crosslinking" of monomer units into a polymer chain, and the finished polymer is dumped from the matrix.

After that, the matrix is ready to assemble a new polymer molecule. It is clear that just as only one coin, one letter can be cast on a given mold, so only one polymer can be "assembled" on a given matrix molecule.

The matrix type of reactions is a specific feature of the chemistry of living systems. They are the basis of the fundamental property of all living things - its ability to reproduce its own kind.

Matrix synthesis reactions include:

1. DNA replication - the process of self-doubling of the DNA molecule, carried out under the control of enzymes. On each of the DNA strands formed after the breaking of hydrogen bonds, with the participation of the enzyme DNA polymerase, a daughter strand of DNA is synthesized. The material for synthesis is free nucleotides present in the cytoplasm of cells.

The biological meaning of replication lies in the exact transfer of hereditary information from the parent molecule to the daughter ones, which normally occurs during the division of somatic cells.

The DNA molecule consists of two complementary strands. These chains are held together by weak hydrogen bonds that can be broken by enzymes.

The molecule is capable of self-doubling (replication), and on each old half of the molecule a new half of it is synthesized.

In addition, an mRNA molecule can be synthesized on a DNA molecule, which then transfers the information received from DNA to the site of protein synthesis.

Information transfer and protein synthesis follow a matrix principle, comparable to the work of a printing press in a printing house. Information from DNA is copied over and over again. If errors occur during copying, they will be repeated in all subsequent copies.

True, some errors in the copying of information by a DNA molecule can be corrected - the process of eliminating errors is called reparation. The first of the reactions in the process of information transfer is the replication of the DNA molecule and the synthesis of new DNA strands.

2. transcription - the synthesis of i-RNA on DNA, the process of removing information from a DNA molecule synthesized on it by an i-RNA molecule.

I-RNA consists of one strand and is synthesized on DNA in accordance with the rule of complementarity with the participation of an enzyme that activates the beginning and end of the synthesis of the i-RNA molecule.

The finished mRNA molecule enters the cytoplasm on the ribosomes, where the synthesis of polypeptide chains takes place.

3. translation - protein synthesis on i-RNA; the process of translating the information contained in the nucleotide sequence of an mRNA into the sequence of amino acids in a polypeptide.

4. Synthesis of RNA or DNA on RNA viruses

Thus, protein biosynthesis is one of the types of plastic exchange, during which the hereditary information encoded in DNA genes is realized into a certain sequence of amino acids in protein molecules.

Protein molecules are essentially polypeptide chains made up of individual amino acids. But amino acids are not active enough to connect with each other on their own. Therefore, before they combine with each other and form a protein molecule, amino acids must be activated. This activation occurs under the action of special enzymes.

As a result of activation, the amino acid becomes more labile and binds to t-RNA under the action of the same enzyme. Each amino acid corresponds to a strictly specific t-RNA, which finds its “own” amino acid and transfers it to the ribosome.

Consequently, the ribosome receives various activated amino acids connected to their tRNAs. The ribosome is like a conveyor for assembling a protein chain from various amino acids entering it.

Simultaneously with t-RNA, on which its own amino acid "sits", a "signal" from DNA, which is contained in the nucleus, enters the ribosome. In accordance with this signal, one or another protein is synthesized in the ribosome.

The directing influence of DNA on protein synthesis is not carried out directly, but with the help of a special intermediary - matrix or messenger RNA (mRNA or mRNA), which is synthesized in the nucleus under the influence of DNA, therefore its composition reflects the composition of DNA. The RNA molecule is, as it were, a cast from the form of DNA. The synthesized mRNA enters the ribosome and, as it were, transfers to this structure a plan - in what order the activated amino acids that have entered the ribosome should be connected to each other in order to synthesize a certain protein. Otherwise, the genetic information encoded in DNA is transferred to mRNA and then to protein.

The mRNA molecule enters the ribosome and stitches it. That section of it, which is currently in the ribosome, defined by a codon (triplet), interacts in a completely specific way with a triplet (anticodon) suitable for its structure in the transfer RNA, which brought the amino acid into the ribosome.

Transfer RNA with its amino acid approaches a specific codon of i-RNA and connects to it; another t-RNA with a different amino acid joins the next, neighboring section of the i-RNA, and so on until the entire chain of the i-RNA is read, until all the amino acids are strung in the appropriate order, forming a protein molecule.

And t-RNA, which delivered the amino acid to a certain site of the polypeptide chain, is released from its amino acid and leaves the ribosome. matrix cell nucleic gene

Then again in the cytoplasm, the desired amino acid can join it, and it will again transfer it to the ribosome.

In the process of protein synthesis, not one, but several ribosomes, polyribosomes, are involved simultaneously.

The main stages of the transfer of genetic information:

synthesis on DNA as on an i-RNA template (transcription)

synthesis in the ribosomes of the polypeptide chain according to the program contained in the i-RNA (translation).

The stages are universal for all living beings, but the temporal and spatial relationships of these processes differ in pro- and eukaryotes.

In eukaryotes, transcription and translation are strictly separated in space and time: the synthesis of various RNAs occurs in the nucleus, after which the RNA molecules must leave the nucleus, passing through the nuclear membrane. Then, in the cytoplasm, RNA is transported to the site of protein synthesis - ribosomes. Only after that comes the next stage - translation.

In prokaryotes, transcription and translation occur simultaneously.

Thus, the place of synthesis of proteins and all enzymes in the cell are ribosomes - they are, as it were, "factories" of the protein, as if an assembly shop, where all the materials necessary to assemble the polypeptide chain of a protein from amino acids come. The nature of the synthesized protein depends on the structure of the i-RNA, on the order of the nucleoids in it, and the structure of the i-RNA reflects the structure of the DNA, so that in the end the specific structure of the protein, i.e. the order in which various amino acids are arranged in it, depends on the order of arrangement nucleoids in DNA, from the structure of DNA.

The stated theory of protein biosynthesis was called the matrix theory. This theory is called matrix because nucleic acids play, as it were, the role of matrices in which all information is recorded regarding the sequence of amino acid residues in a protein molecule.

The creation of the matrix theory of protein biosynthesis and the deciphering of the amino acid code is the largest scientific achievement of the 20th century, the most important step towards elucidating the molecular mechanism of heredity.

Algorithm for solving problems.

Type 1. DNA self-copying. One of the DNA chains has the following sequence of nucleotides: AGTACCGATACCTCGATTTACG... What nucleotide sequence does the second chain of the same molecule have? To write the nucleotide sequence of the second strand of a DNA molecule, when the sequence of the first strand is known, it is enough to replace thymine with adenine, adenine with thymine, guanine with cytosine, and cytosine with guanine. Having made such a replacement, we obtain the sequence: TACCTGGCTATGAGCCTAAATG... Type 2. Protein coding. The amino acid chain of the ribonuclease protein has the following beginning: lysine-glutamine-threonine-alanine-alanine-alanine-lysine... From what sequence of nucleotides does the gene corresponding to this protein begin? To do this, use the table of the genetic code. For each amino acid, we find its code designation in the form of the corresponding trio of nucleotides and write it out. Arranging these triplets one after another in the same order as the corresponding amino acids go, we obtain the formula for the structure of the messenger RNA section. As a rule, there are several such triples, the choice is made according to your decision (but only one of the triples is taken). There may be several solutions, respectively. AAACAAAATSUGTSGGTSUGTSGAAG Type 3. Decoding of DNA molecules. What amino acid sequence does the protein begin with, if it is encoded by such a nucleotide sequence: ACGCCCATGGCCGGT ... By the principle of complementarity, we find the structure of the informational RNA site formed on this segment of the DNA molecule: UGCGGGUACCCGGCCA ... Then we turn to the table of the genetic code and for each trio of nucleotides, starting from the first, we find and write out the amino acid corresponding to it: Cysteine-glycine-tyrosine-arginine-proline-...

2. Biology abstract in grade 10 "A" on the topic: Protein biosynthesis

Purpose: To introduce the processes of transcription and translation.

Educational. Introduce the concepts of gene, triplet, codon, DNA code, transcription and translation, explain the essence of the process of protein biosynthesis.

Developing. Development of attention, memory, logical thinking. Training of spatial imagination.

Educational. Education of a culture of work in the classroom, respect for the work of others.

Equipment: Board, tables on protein biosynthesis, magnetic board, dynamic model.

Literature: textbooks Yu.I. Polyansky, D.K. Belyaeva, A.O. Ruvinsky; "Fundamentals of Cytology" O.G. Mashanova, "Biology" V.N. Yarygina, "Genes and genomes" Singer and Berg, school notebook, N.D. Lisova studies. A manual for grade 10 "Biology".

Methods and methodological techniques: story with elements of conversation, demonstration, testing.

	Material test. Distribute leaflets and test cases. All notebooks and textbooks are closed. 1 mistake with the 10th question done is 10, with the 10th not done - 9, etc.
	Write down the topic of today's lesson: Protein biosynthesis. The entire DNA molecule is divided into segments encoding the amino acid sequence of one protein. Write down: a gene is a section of a DNA molecule that contains information about the sequence of amino acids in one protein.
	DNA code. We have 4 nucleotides and 20 amino acids. How to compare them? If 1 nucleotide encoded 1 a/k, => 4 a/k; if 2 nucleotides - 1 a / c - (how many?) 16 amino acids. Therefore, 1 amino acid encodes 3 nucleotides - a triplet (codon). Count how many combinations are possible? - 64 (3 of them are punctuation marks). Sufficient and even in excess. Why excess? 1 a / c can be encoded in 2-6 triplets to improve the reliability of storage and transmission of information. Properties of the DNA code. 1) Code triplet: 1 amino acid encodes 3 nucleotides. 61 triplet encodes a / k, with one AUG indicating the beginning of the protein, and 3 - punctuation marks. 2) The code is degenerate - 1 a/k encodes 1,2,3,4,6 triplets 3) The code is unambiguous - 1 triplet only 1 a / c 4) Non-overlapping code - from 1 to the last triplet, the gene encodes only 1 protein 5) The code is continuous - there are no punctuation marks inside the gene. They are only between genes. *6) The code is universal - all 5 kingdoms have the same code. Only in mitochondria are 4 triplets different.* Think at home and tell me why?
	All information is contained in DNA, but DNA itself does not participate in protein biosynthesis. Why? Information is written to i-RNA, and already on it in the ribosome there is a synthesis of a protein molecule. DNA RNA protein. Tell me if there are organisms that have the reverse order: RNA DNA?
	Biosynthetic Factors: The presence of information encoded in the DNA gene. The presence of an intermediary i-RNA for the transfer of information from the nucleus to the ribosomes. The presence of an organelle - a ribosome. Availability of raw materials - nucleotides and a / c Presence of tRNA to deliver amino acids to the assembly site The presence of enzymes and ATP (Why?)
	biosynthetic process. Transcription. (show on the model) Rewriting the sequence of nucleotides from DNA to mRNA. The biosynthesis of RNA molecules goes to DNA according to the principles: Matrix synthesis Complimentary DNA and RNA DNA is cleaved with the help of a special enzyme, another enzyme begins to synthesize mRNA on one of the chains. The size of an mRNA is 1 or more genes. I-RNA leaves the nucleus through nuclear pores and goes to the free ribosome.
	Broadcast. Synthesis of polypeptide chains of proteins, carried out on the ribosome. Having found a free ribosome, mRNA is threaded through it. I-RNA enters the ribosome as an AUG triplet. At the same time, only 2 triplets (6 nucleotides) can be in the ribosome. We have nucleotides in the ribosome, now we need to somehow deliver a / c there. With the help of what? - t-RNA. Consider its structure. Transfer RNAs (tRNAs) are approximately 70 nucleotides long. Each t-RNA has an acceptor end to which an amino acid residue is attached, and an adapter end carrying a triple of nucleotides complementary to any codon of the i-RNA, therefore this triplet was called an anticodon. How many types of tRNA do you need in a cell? The t-RNA with the corresponding a/k tries to join the m-RNA. If the anticodon is complementary to the codon, then a bond is attached and a bond occurs, which serves as a signal for the movement of the ribosome along the mRNA strand by one triplet. A / c joins the peptide chain, and t-RNA, freed from a / c, enters the cytoplasm in search of another such a / c. The peptide chain thus lengthens until translation ends and the ribosome jumps off the mRNA. Several ribosomes can be placed on one mRNA (in the textbook, the figure in paragraph 15). The protein chain enters the EPS, where it acquires a secondary, tertiary or quaternary structure. The whole process is shown in the textbook Fig. 22 - at home, find an error in this figure - get 5) Tell me, how do these processes go about prokaryotes if they do not have a nucleus?
	regulation of biosynthesis. Each chromosome is linearly divided into operons consisting of a regulator gene and a structural gene. The signal for the regulator gene is either the substrate or end products.
	1. Find the amino acids encoded in the DNA fragment. T-A-C-G-A-A-A-A-T-C-A-A-T-C-T-C-U-A-U- Solution: A-U-G-C-U-U-U-U-A-G-U-U-A-G-A-G-A-U-A- MET LEI LEI VAL ARG ASP It is necessary to compose a fragment of i-RNA and break it into triplets. 2. Find t-RNA anticodons to transfer the indicated amino acids to the assembly site. Met, three, hair dryer, arg.
	Homework paragraph 29.